spacer
spacer

PDBsum entry 1r5c

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1r5c
Jmol
Contents
Protein chains
124 a.a. *
Ligands
CPA ×2
Waters ×91
* Residue conservation analysis
PDB id:
1r5c
Name: Hydrolase
Title: X-ray structure of the complex of bovine seminal ribonuclease swapping dimer with d(cpa)
Structure: Ribonuclease, seminal. Chain: a, b. Synonym: seminal rnase, s-rnase, ribonuclease bs-1. Ec: 3.1.27.5
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.190     R-free:   0.242
Authors: A.Merlino,L.Vitagliano,F.Sica,A.Zagari,L.Mazzarella
Key ref: A.Merlino et al. (2004). Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer. Biopolymers, 73, 689-695. PubMed id: 15048772
Date:
10-Oct-03     Release date:   13-Apr-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00669  (RNS_BOVIN) -  Seminal ribonuclease
Seq:
Struc:
150 a.a.
124 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.5  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
Biopolymers 73:689-695 (2004)
PubMed id: 15048772  
 
 
Population shift vs induced fit: the case of bovine seminal ribonuclease swapping dimer.
A.Merlino, L.Vitagliano, F.Sica, A.Zagari, L.Mazzarella.
 
  ABSTRACT  
 
Bovine seminal ribonuclease (BS-RNase) is a unique member of the pancreatic-like ribonuclease superfamily. This enzyme exists as two conformational isomers with distinctive biological properties. The structure of the major isomer is characterized by the swapping of the N-terminal segment (MxM BS-RNase). In this article, the crystal structures of the ligand-free MxM BS-RNase and its complex with 2'-deoxycitidylyl(3',5')-2'-deoxyadenosine derived from isomorphous crystals have been refined. Interestingly, the comparison between this novel ligand-free form and the previously published sulfate-bound structure reveals significant differences. In particular, the ligand-free MxM BS-RNase is closer to the structure of MxM BS-RNase productive complexes than to the sulfate-bound form. These results reveal that MxM BS-RNase presents a remarkable flexibility, despite the structural constraints of the interchain disulfide bridges and the swapping of the N-terminal helices. These findings have important implications to the ligand binding mechanism of MxM BS-RNase. Indeed, a population shift rather than a substrate-induced conformational transition may occur in the MxM BS-RNase ligand binding process.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21205197 N.Thiyagarajan, B.D.Smith, R.T.Raines, and K.R.Acharya (2011).
Functional and structural analyses of N-acylsulfonamide-linked dinucleoside inhibitors of RNase A.
  FEBS J, 278, 541-549.
PDB codes: 2xog 2xoi
21050179 E.Pizzo, A.Merlino, M.Turano, I.Russo Krauss, F.Coscia, A.Zanfardino, M.Varcamonti, A.Furia, C.Giancola, L.Mazzarella, F.Sica, and G.D'Alessio (2010).
A new RNase sheds light on the RNase/angiogenin subfamily from zebrafish.
  Biochem J, 433, 345-355.
PDB codes: 3ljd 3lje 3ln8
  19177350 A.Merlino, G.Avella, S.Di Gaetano, A.Arciello, R.Piccoli, L.Mazzarella, and F.Sica (2009).
Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.
  Protein Sci, 18, 50-57.
PDB code: 3f8g
19280639 A.Merlino, I.Russo Krauss, M.Perillo, C.A.Mattia, C.Ercole, D.Picone, A.Vergara, and F.Sica (2009).
Toward an antitumor form of bovine pancreatic ribonuclease: The crystal structure of three noncovalent dimeric mutants.
  Biopolymers, 91, 1029-1037.
PDB codes: 3fkz 3fl0 3fl1 3fl3
19263489 C.Ercole, R.A.Colamarino, E.Pizzo, F.Fogolari, R.Spadaccini, and D.Picone (2009).
Comparison of the structural and functional properties of RNase A and BS-RNase: A stepwise mutagenesis approach.
  Biopolymers, 91, 1009-1017.  
18161991 E.D.Merkley, B.Bernard, and V.Daggett (2008).
Conformational changes below the Tm: molecular dynamics studies of the thermal pretransition of ribonuclease A.
  Biochemistry, 47, 880-892.  
15728177 A.Merlino, L.Mazzarella, A.Carannante, A.Di Fiore, A.Di Donato, E.Notomista, and F.Sica (2005).
The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase mutants.
  J Biol Chem, 280, 17953-17960.
PDB codes: 1yv4 1yv6 1yv7
15596505 A.Merlino, M.A.Ceruso, L.Vitagliano, and L.Mazzarella (2005).
Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A.
  Biophys J, 88, 2003-2012.  
15647261 D.Picone, A.Di Fiore, C.Ercole, M.Franzese, F.Sica, S.Tomaselli, and L.Mazzarella (2005).
The role of the hinge loop in domain swapping. The special case of bovine seminal ribonuclease.
  J Biol Chem, 280, 13771-13778.
PDB codes: 1y92 1y94
16280619 T.Mamonova, B.Hespenheide, R.Straub, M.F.Thorpe, and M.Kurnikova (2005).
Protein flexibility using constraints from molecular dynamics simulations.
  Phys Biol, 2, S137-S147.  
15192098 F.Sica, A.Di Fiore, A.Merlino, and L.Mazzarella (2004).
Structure and stability of the non-covalent swapped dimer of bovine seminal ribonuclease: an enzyme tailored to evade ribonuclease protein inhibitor.
  J Biol Chem, 279, 36753-36760.
PDB code: 1tq9
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.